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Well, for one thing you have to buy the JVM in addition to the application that you want to run - it's not expensive, but an extra hassle and cost to deal with. It's amazing how little patience people have when they need to put in just a little extra effort.
In addition, I've often found Java applications to be quite resource-intensive, which is probably not ideal for a PocketPC. I'm always having to keep an eye on memory usage on my own PPC as it is.
Pete
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